Tissue fluidity gene signatures and scoring for wound healing analysis. Use when working with EMT, ECM, migration, mechanotransduction, or wound signal genes.
Vim, Cdh1, Cdh2, Snai1, Snai2, Twist1, Zeb1, Zeb2
Fn1, Col1a1, Col3a1, Mmp2, Mmp9, Mmp14, Timp1, Lox, Loxl2
Rac1, Cdc42, Itgb1, Rhoa, Rock1, Rock2, Itga6, Cxcl12, Cxcr4
Yap1, Wwtr1, Piezo1, Trpv4, Lats1, Lats2
Tgfb1, Tgfb2, Tgfb3, Pdgfa, Pdgfb, Fgf2, Vegfa, Wnt5a
fluidity_sets = {
'EMT_signature': ['Vim', 'Cdh1', 'Cdh2', 'Snai1', 'Snai2', 'Twist1', 'Zeb1', 'Zeb2'],
'ECM_remodeling': ['Fn1', 'Col1a1', 'Col3a1', 'Mmp2', 'Mmp9', 'Mmp14', 'Timp1', 'Lox', 'Loxl2'],
'Cell_migration': ['Rac1', 'Cdc42', 'RhoA', 'Itgb1', 'Itga6', 'Cxcl12', 'Cxcr4'],
'Mechanotransduction': ['Yap1', 'Wwtr1', 'Piezo1', 'Trpv4', 'Lats1', 'Lats2'],
'Wound_signals': ['Tgfb1', 'Tgfb2', 'Tgfb3', 'Pdgfa', 'Pdgfb', 'Fgf2', 'Vegfa', 'Wnt5a'],
}
for name, genes in fluidity_sets.items():
available = [g for g in genes if g in adata.var_names]
if available:
sc.tl.score_genes(adata, gene_list=available, score_name=f'fluidity_{name}')
fluidity_sets <- list(
EMT = c("Vim", "Cdh1", "Cdh2", "Snai1", "Snai2", "Twist1", "Zeb1", "Zeb2"),
ECM = c("Fn1", "Col1a1", "Col3a1", "Mmp2", "Mmp9", "Mmp14", "Timp1", "Lox"),
Migration = c("Rac1", "Cdc42", "RhoA", "Itgb1", "Itga6"),
Mechanotx = c("Yap1", "Piezo1", "Trpv4", "Lats1", "Lats2"),
WoundSig = c("Tgfb1", "Pdgfa", "Vegfa", "Wnt5a", "Fgf2")
)
for (name in names(fluidity_sets)) {
genes <- fluidity_sets[[name]]
available <- genes[genes %in% rownames(sobj)]
if (length(available) >= 2) {
sobj <- AddModuleScore(sobj, features = list(available), name = paste0("fluidity_", name))
}
}